Integrated metabarcoding and culturomics reveal the rot-suppressive rhizoplane mycobiome of cassava across contrasting agroecological habitats

Abstract

Introduction Cassava stem and root rot caused by Fusarium falciforme (Fusarium solani species complex) constrains production in waterlogged tropical systems. In Kerala, India, disease endemicity differs markedly between wetlands and uplands, yet the ecological basis of this variation remains unresolved. We tested whether rhizoplane mycobiome structure and functional stability govern pathogen suppression across these habitats. Methods Rhizoplane fungal communities from healthy and diseased plants in endemic wetlands and non-endemic uplands were profiled using Internal Transcribed Spacer amplicon sequencing, complemented by culture-dependent isolation and soil physicochemical analyses. Core taxa were identified through microbiome modeling and validated by ITS sequencing of isolates. Antagonistic activity against F. falciforme was assessed using dual-culture assays and greenhouse validation. Results Quality filtering retained 847,760, 1,037,834, and 539,722 high-quality paired-end reads from the upland, wetland diseased, and wetland healthy rhizoplane samples, respectively. Healthy wetland rhizoplanes exhibited higher diversity and stability than diseased counterparts (Shannon +20%; inverse Simpson +60%). Disease was associated with diversity collapse and enrichment of opportunistic taxa, whereas upland communities remained distinct and stable. A conserved core mycobiome dominated by the members of Pichia, Aspergillus, Sugiyamaella, and Fusarium was identified, with Penicillium and Talaromyces forming an extended functional core. Isolates of Penicillium oxalicum and Talaromyces pinophilus inhibited F. falciforme by >90% in vitro and reduced disease incidence to 0% in greenhouse assays, matching chemical control. Soil acidity and nutrient imbalance were strongly associated with mycobiome disruption and disease. Discussion Disease emergence coincided with loss of rhizoplane diversity and depletion of key antagonists, indicating failure of microbial resistance under edaphic stress. The consistent identification and validation of P. oxalicum and T. pinophilus as keystone antagonists support their functional role in pathogen suppression. Integrating microbiome conservation with soil health restoration offers a robust, climate-resilient strategy for managing cassava stem and root rot in tropical agroecosystems.